Genome-wide association and genomic prediction for host response to porcine reproductive and respiratory syndrome virus infection.
Genome-wide association and genomic prediction for host response to porcine reproductive and respiratory syndrome virus infection.
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全基因组的关联和基因组预测，用于宿主对猪生殖和呼吸道综合征病毒感染的反应。
DOI：
10.1186/1297-9686-46-18
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发表时间：
2014-03-04
期刊：
影响因子：
--
通讯作者：
Dekkers JC
中科院分区：
文献类型：
--
作者：
Boddicker NJ;Bjorkquist A;Rowland RR;Lunney JK;Reecy JM;Dekkers JC
猪繁殖与呼吸综合征（PRRS）是养猪业中最具经济意义的疾病，宿主遗传学已被证明在PRRS中起作用。猪染色体（SSC）4上的一个区域先前已被报道与实验感染PRRS病毒（PRRSV）的猪的血清病毒血症和体重增加有很强的关联。本文的目的是鉴定与有利表型相关的单倍型，研究与宿主对PRRSV的反应相关的其他基因组区域，并基于SSC 4区域和基因组的其余部分确定基因组估计育种值（GEBV）的预测能力。表型数据和60 K SNP基因型从8个试验的约200头猪从不同的商业杂交来解决这些目标。在8项试验中，病毒载量（VL，感染后0 - 21天对数转换血清病毒血症曲线下面积）和感染后42天体重增加（WG）的遗传度估计值分别为0.44和0.29。在染色体4、X和1上鉴定了与VL相关的基因组区域。在第4、5和7号染色体上鉴定了与WG相关的基因组区域。除了SSC 4区域，与这两个性状相关的区域各自解释了不到3%的遗传方差。由于在SSC 4区域中的强连锁不平衡，在所有群体中仅鉴定出19种独特的单倍型，其中4种与有利的表型相关。通过交叉验证，基于SSC 4区域的EBV准确性很高（0.55），而基因组的其余部分在人群中的预测能力很小（0.09）。与生长猪对PRRSV感染的反应相关的性状主要由基因组区域控制，影响相对较小，但SSC 4除外。与基因组的其余部分相比，基于SSC 4区域的EBV的准确性较高。这些结果表明，对SSC 4区域的选择可能会降低PRRS对生长猪的影响，最终降低这种疾病的经济影响。
Host genetics has been shown to play a role in porcine reproductive and respiratory syndrome (PRRS), which is the most economically important disease in the swine industry. A region on Sus scrofa chromosome (SSC) 4 has been previously reported to have a strong association with serum viremia and weight gain in pigs experimentally infected with the PRRS virus (PRRSV). The objective here was to identify haplotypes associated with the favorable phenotype, investigate additional genomic regions associated with host response to PRRSV, and to determine the predictive ability of genomic estimated breeding values (GEBV) based on the SSC4 region and based on the rest of the genome. Phenotypic data and 60 K SNP genotypes from eight trials of ~200 pigs from different commercial crosses were used to address these objectives. Across the eight trials, heritability estimates were 0.44 and 0.29 for viral load (VL, area under the curve of log-transformed serum viremia from 0 to 21 days post infection) and weight gain to 42 days post infection (WG), respectively. Genomic regions associated with VL were identified on chromosomes 4, X, and 1. Genomic regions associated with WG were identified on chromosomes 4, 5, and 7. Apart from the SSC4 region, the regions associated with these two traits each explained less than 3% of the genetic variance. Due to the strong linkage disequilibrium in the SSC4 region, only 19 unique haplotypes were identified across all populations, of which four were associated with the favorable phenotype. Through cross-validation, accuracies of EBV based on the SSC4 region were high (0.55), while the rest of the genome had little predictive ability across populations (0.09). Traits associated with response to PRRSV infection in growing pigs are largely controlled by genomic regions with relatively small effects, with the exception of SSC4. Accuracies of EBV based on the SSC4 region were high compared to the rest of the genome. These results show that selection for the SSC4 region could potentially reduce the effects of PRRS in growing pigs, ultimately reducing the economic impact of this disease.
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